GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Marinobacter adhaerens HP15

Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate GFF4001 HP15_3941 fatty oxidation complex alpha subunit

Query= reanno::BFirm:BPHYT_RS13545
         (706 letters)



>FitnessBrowser__Marino:GFF4001
          Length = 702

 Score =  658 bits (1698), Expect = 0.0
 Identities = 347/701 (49%), Positives = 471/701 (67%), Gaps = 10/701 (1%)

Query: 7   ADVVSRELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIA 66
           ++VVS    G + ++T+++ PVNAL   VR GLLAA+E    D    A+L+V  GR FIA
Sbjct: 7   SEVVSYNREGNIGVITVNYPPVNALGQAVRSGLLAALEQGQKDTEARALLLVCEGRTFIA 66

Query: 67  GADIREFGKPPVPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKL 126
           GADIREFGKP   P+LP + N  E   KP+VAAIHG ALGGGLE AL+ HYR+A+  AK+
Sbjct: 67  GADIREFGKPMQEPTLPTLVNTFENSDKPLVAAIHGTALGGGLETALSCHYRVAISSAKV 126

Query: 127 GLPEVQLGLLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILA 186
           GLPEV+LGLLPGAGGTQR PRL GA+ AL++I +G    AK+ALA G++D +   DDI A
Sbjct: 127 GLPEVKLGLLPGAGGTQRLPRLTGARKALEMITTGEFVGAKDALALGILDAVEEGDDIRA 186

Query: 187 EGLAYVHELLAAHAPVRRTRDAAALSDRAASLAAVATARAETAKKSRGLFSPLKIVDAVE 246
            G+AY  +++    PVRR RD     +           R E  K++RGLFSP K VDAVE
Sbjct: 187 VGMAYAQKVVDEGKPVRRVRDITDKIEADKGSDVFDQFRDELKKRARGLFSPFKCVDAVE 246

Query: 247 AAIEQPFDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRAAKP-RTLNTIGV 305
           AA   PFDEG++ ER+LF+EC++SPQRAGLIH+FF EREV K        P R + ++G+
Sbjct: 247 AAFNLPFDEGMKRERELFMECMESPQRAGLIHSFFGEREVSKVKGLSKDTPVRDVKSVGI 306

Query: 306 VGGGTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALM 365
           +G GTMG GIA+  ++ G+PVT++E    +L +G A I + Y+    KG+L+ E+    M
Sbjct: 307 IGAGTMGGGIAMNFVNVGIPVTIVEVKQEALDKGLAIIRRNYENSAKKGKLTQEQVEQRM 366

Query: 366 SRWSGSTSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALAS 425
           +  + S +YD     DLVIEAVFE++A+K+ +FA+LD VCK GA+LA+NTS LDID +AS
Sbjct: 367 ALITPSLTYDDFRDVDLVIEAVFENMAIKKEIFAKLDEVCKPGAILASNTSTLDIDEIAS 426

Query: 426 SVSRPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFI 485
           +  RP DV+G+HFFSPAN+MKLLE V   + S +V AT   +AKK++K  V  G C GF+
Sbjct: 427 ATKRPEDVVGMHFFSPANVMKLLENVRGSKTSDEVKATVMAVAKKIKKVGVMVGNCYGFV 486

Query: 486 GNRVLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAAR-KRRAA 544
           GNR+L    + A +++++GA+P Q+D  +   GFPMG F + DLAG D+G+  R +RR A
Sbjct: 487 GNRMLHKRGTEAMSLVDEGATPQQVDKVLTDLGFPMGQFAMSDLAGIDVGYRIREERRKA 546

Query: 545 TRNPAARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITP 604
             +  A ++   D+L E+G  GQK+  G Y Y EGSR   PDPEVE +I+  R   GITP
Sbjct: 547 GEDIPASWM---DKLAEQGRLGQKTQAGVYKYEEGSRKPIPDPEVEQLIEQFRKEQGITP 603

Query: 605 RSFTDEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMVG 664
           R  T++EI+ R +  MINEGA ++ E IA RPLD+D+ ++YGYGFP YRGGPM +AD  G
Sbjct: 604 REITNQEILERCVYVMINEGAKILEEGIADRPLDIDIVWIYGYGFPAYRGGPMFWADQEG 663

Query: 665 LPKILADIREFAKEDPL---FWKPSPLLIELVERGADFASL 702
           L  IL+ ++++  +D +    W+P+ LL +LV  G  FA L
Sbjct: 664 LDTILSAVKKY--QDTVGGEQWEPAALLEKLVAEGRKFADL 702


Lambda     K      H
   0.320    0.136    0.392 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1115
Number of extensions: 43
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 706
Length of database: 702
Length adjustment: 39
Effective length of query: 667
Effective length of database: 663
Effective search space:   442221
Effective search space used:   442221
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory